Method of predicting a predisposition to QT prolongation

ABSTRACT

The present invention describes an association between genetic polymorphisms in the BAI3 gene and a predisposition to prolongation of the QT interval, and provides related methods for the prediction of such a predisposition, the administration of QT interval-prolonging compounds to individuals having such a predisposition, and determining whether a compound is capable of inducing QT prolongation.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of co-pending U.S. application Ser. No. 14/694,142, filed Apr. 23, 2015, which is a continuation of then-co-pending U.S. application Ser. No. 13/263,077, filed Oct. 5, 2011, which is a US National Stage application under 35 USC 371 of PCT/US2010/29945, filed Apr. 5, 2010, which claims the benefit of U.S. Provisional Patent Application No. 61/167,140, filed Apr. 6, 2009, each of which is incorporated herein as though fully set forth.

BACKGROUND OF THE INVENTION 1. Technical Field

The invention relates generally to a method of predicting an individual's predisposition to QT prolongation, and more particularly, to a method of predicting such predisposition based on a sequence of the individual's BAI3 (brain-specific angiogenesis inhibitor 3) gene.

2. Background

Prolongation of the electrocardiographic QT interval (the time between the start of the Q wave and the end of the T wave) is referred to as long QT syndrome (LQTS). LQTS may comprise a genetic component. In some patients with LQTS, QT prolongation can be a chronic condition. In some persons, LQTS may be induced by the administration of an active pharmaceutical ingredient that prolongs the QT interval. A number of compounds are believed to be capable of prolonging the QT interval. These include amiodarone, arsenic trioxide, bepridil, chloroquine, chlorpromazine, cisapride, clarithromycin, disopyramide, dofetilide, domperidone, droperidol, erythromycin, halofantrine, haloperidol, ibutilide, iloperidone, levomethadyl, mesoridazine, methadone, pentamidine, pimozide, procainamide, quinidine, sotalol, sparfloxacin, and thioridazine.

Other compounds are suspected of being capable of prolonging the QT interval, although such prolongation has not been definitively established. These include alfuzosin, amantadine, azithromycin, chloral hydrate, clozapine, dolasetron, felbamate, flecainide, foscarnet, fosphenytoin, gatifloxacin, gemifloxacin, granisetron, indapamide, isradipine, levofloxacin, lithium, moexipril, moxifloxacin, nicardipine, octreotide, ofloxacin, ondansetron, quetiapine, ranolazine, risperidone, roxithromycin, tacrolimus, tamoxifen, telithromycin, tizanidine, vardenafil, venlafaxine, voriconazole, and ziprasidone.

Individuals at risk of suffering LQTS are advised not to use still other compounds, due to the possibility that they may prolong the QT interval. These include albuterol, amitriptyline, amoxapine, amphetamine, dextroamphetamine, atomoxetine, chloroquine, ciprofloxacin, citalopram, clomipramine, cocaine, desipramine, dexmethylphenidate, dobutamine, dopamine, doxepin, ephedrine, epinephrine, fenfluramine, fluconazole, fluoxetine, galantamine, imipramine, isoproterenol, itraconazole, ketoconazole, levalbuterol, metaproterenol, methylphenidate, mexiletine, midodrine, norepinephrine, nortriptyline, paroxetine, phentermine, phenylephrine, phenylpropanolamine, protriptyline, pseudoephedrine, ritodrine, salmeterol, sertraline, sibutramine, solifenacin, terbutaline, tolterodine, trimethoprim-sulfa, and trimipramine.

Shiratsuchi et al. mapped the BAI3 gene to 6q12 by fluorescence in situ hybridization. They found that BAI3 expression was absent in 2 of 9 glioblastoma cell lines examined and was significantly reduced in 3 of the remaining 7. These findings suggested that the gene may play an important role in suppression of glioblastoma. Shiratsuchi et al., Cloning and characterization of BAI2 and BAI3, novel genes homologous to brain-specific angiogenesis inhibitor 1 (BAI1), Cytogenet. Cell Genet. 79: 103-108, 1997. PubMed ID: 9533023.

SUMMARY OF THE INVENTION

The present invention describes an association between genetic polymorphisms in the BAI3 gene and a predisposition to prolongation of the QT interval, and provides related methods for the diagnosis of such predisposition and for the administration of QT interval-prolonging compounds to individuals having such a predisposition.

A first aspect of the invention provides a method of administering to an individual a compound capable of prolonging the individual's QT interval, the method comprising determining at least a portion of an individual's BAI3 gene sequence; and in the case that a portion of the individual's BAI3 sequence is associated with an increased risk of QT prolongation, administering to the individual a quantity of the compound less than would be administered to an individual having a BAI3 gene sequence not associated with an increased risk of QT prolongation, or electing instead to treat the individual with a different compound not known to be associated with QT prolongation.

A second aspect of the invention provides a method of determining whether or not an individual is predisposed to prolongation of the QT interval, the method comprising: determining at least a portion of an individual's BAI3 gene sequence.

A third aspect of the invention provides a method of administering a compound capable of prolonging a QT interval to an individual suffering from long QT syndrome (LQTS), the method comprising: determining at least a portion of an individual's BAI3 gene sequence; and administering to the individual a quantity of the compound based on the individual's BAI3 gene sequence.

A fourth aspect of the invention provides a method of administering to an individual a compound capable of prolonging the individual's QT interval, the method comprising: characterizing an expression product of an individual's BAI3 gene; and in the case that the characterized expression product is associated with an increased risk of QT prolongation, administering to the individual a quantity of the compound less than would be administered to an individual having an expression product not associated with an increased risk of QT prolongation. Expression products of the BAI3 gene may include, for example, mRNA and protein including any isoform of the mRNA and protein.

A fifth aspect of the invention provides a method of determining whether an individual is predisposed to prolongation of the QT interval, the method comprising: characterizing an expression product of an individual's BAI3 gene.

A sixth aspect of the invention provides a method of administering a compound capable of prolonging a QT interval to an individual suffering from long OT syndrome (LQTS), the method comprising: characterizing an expression product of an individual's BAI3 gene; and administering to the individual a quantity of the compound based on the characterized expression product.

A seventh aspect of the invention provides a method of determining whether a compound is capable of prolonging QT interval in an individual, the method comprising: measuring an expression product of the individual's BAI3 gene; administering to the individual a quantity of the compound; remeasuring the expression product of the individual's BAI3 gene; and determining whether the compound is capable of prolonging the individual's QT interval based on a difference in the measurements of the expression product of the individual's BAI3 gene.

An eighth aspect of the invention provides a method of determining whether a compound is capable of prolonging a QT interval in an individual, the method comprising: measuring a QT interval of each of a plurality of test organisms, the plurality including a first test organism having a BAI3 genotype associated with a predisposition for prolongation of QT interval and a second organism having BAI3 genotype not associated with a predisposition for prolongation of QT interval; administering a quantity of the compound to each of the plurality of test organisms; remeasuring a QT interval of at least the first test organism; and determining that the compound is capable of prolonging a QT interval in an individual in the case that the remeasured QT interval is greater than the measured QT interval. Test organisms may include, for example, humans, animal models, and/or cell lines.

DETAILED DESCRIPTION OF THE INVENTION

As indicated above, the invention provides a method of predicting an individual's predisposition to QT prolongation based on the sequence of the individual's BAI3 (brain-specific angiogenesis inhibitor 3) gene.

At least one single nucleotide polymorphisms (SNPs) within the BAI3 gene has been found to have a significant correlation to a predisposition to drug-induced QT prolongation. Table 1, below, shows such SNPs and the genotypes associated with QT prolongation following the administration of iloperidone.

TABLE 1 BAI3 SNP Genotypes and QT Prolongation Following Administration of Iloperidone Lowest QTc Allele Allele Affymetrix SNP No. rs_number¹ Position² change P value³ A B SNP_A-2294948 rs6907911 66612404 AA 0.837187746 A G SNP_A-2258041 rs9354308 66622074 BB 0.415144836 A G SNP_A-2083440 rs9342503 66622157 AA 0.412264811 A G SNP_A-1940079 rs9360161 66622178 BB 0.412264811 C T SNP_A-1845971 rs9453460 66634103 AA 0.197828529 C G SNP_A-4205738 rs1938073 66640108 BB 0.195785046 C G SNP_A-1952116 rs9453462 66640212 BB 0.294769123 A G SNP_A-1950470 rs9354319 66640377 AA 0.203308108 A G SNP_A-2031185 rs9360166 66647695 AA 0.211999573 C T SNP_A-1852739 rs9345711 66648168 BB 0.182813178 C T SNP_A-1986260 rs1499706 66650136 AA 0.203308108 A G SNP_A-4233183 rs9294661 66652692 AA 0.195937985 A C SNP_A-2143412 rs2211636 66653536 AA 0.284364882 A G SNP_A-1986261 rs10498838 66655659 AA 0.090119392 A G SNP_A-1986262 rs10944853 66655705 BB 0.165784125 A C SNP_A-2055599 rs4031876 66660982 AA 0.203308108 A G SNP_A-4238270 rs1938065 66665338 AA 0.209978111 A C SNP_A-1874775 rs9363486 66672272 BB 0.167094675 A G SNP_A-4259425 rs6939062 66690502 nonBB 0.108494901 C T SNP_A-1986264 rs767069 66703267 AA 0.384883462 C T SNP_A-4218993 rs9453519 66705009 nonBB 0.293953686 A G SNP_A-2243416 rs12201218 66710340 nonAA 0.102771404 C T SNP_A-2056924 rs1872309 66717153 nonBB 0.07131535 A C SNP_A-1986265 rs9360172 66727706 AA 0.207084549 C G SNP_A-2025233 rs12215007 66727729 nonAA 0.568115276 C T SNP_A-2175275 rs9445635 66729650 BB 0.175249933 A C SNP_A-4290814 rs9445639 66756421 BB 0.112744744 A C SNP_A-2043165 rs6455065 66758480 nonAB 0.642014714 A G SNP_A-1873370 rs12202805 66760624 nonAA 0.389285087 A G SNP_A-2224620 rs1484568 66763186 nonAB 0.316749746 A T SNP_A-4246307 rs10944874 66808801 AA 0.83099018 C T SNP_A-1805979 rs6455070 66812637 nonAA 0.417875055 A T SNP_A-1791501 rs4618506 66813610 nonAA 0.641629996 A C SNP_A-1838473 rs17527218 66820787 nonAA 0.383655145 A G SNP_A-2245001 rs207078 66826775 AA 0.654341043 G T SNP_A-4239295 rs207079 66827183 AB 0.381183271 C T SNP_A-1956980 rs9363514 66833851 nonBB 0.095955147 A T SNP_A-1986267 rs207114 66848424 nonAA 0.282870767 C T SNP_A-1986268 rs207113 66848468 AA 0.072630039 A C SNP_A-4237915 rs704516 66860616 AA 0.069587818 G T SNP_A-2131968 rs9354370 66864930 BB 0.393304106 C T SNP_A-4246739 rs1738969 66865099 BB 0.130424314 A G SNP_A-2043489 rs7741060 66867525 nonAB 0.782369018 A C SNP_A-2185988 rs3846808 66875325 nonAA 0.390679421 A G SNP_A-2272880 rs7771233 66876505 AA 0.38734038 A G SNP_A-1921295 rs9345762 66876642 AA 0.072761868 A G SNP_A-1838152 rs4710311 66879944 AB 0.127063917 C T SNP_A-2042426 rs4710564 66880199 AB 0.137081364 A G SNP_A-2311392 rs7758063 66888526 BB 0.366283465 C T SNP_A-2073437 rs3899423 66892006 nonAA 0.449112256 A G SNP_A-2105755 rs1304672 66904694 nonBB 0.395107519 A G SNP_A-1956578 rs866452 66906657 nonAA 0.40041906 A T SNP_A-4250392 rs851587 66907832 BB 0.262346635 C T SNP_A-1986271 rs1100978 66908163 nonAA 0.743714604 A G SNP_A-1922936 rs7757797 66916159 nonAB 0.877896214 A C SNP_A-1870283 rs9342529 66922328 nonAA 0.187735651 A G SNP_A-2209298 rs7753158 66932354 nonAA 0.320327884 A C SNP_A-1781066 rs851593 66932504 nonBB 0.323319617 C T SNP_A-2314765 rs9354390 66946883 nonBB 0.1514543 C T SNP_A-2102203 rs9354391 66946904 nonBB 0.386459086 C T SNP_A-1986272 rs9294684 66954310 nonBB 0.380678502 A C SNP_A-1816063 rs9363544 66955520 nonAA 0.536748257 C T SNP_A-4240260 rs9345777 66956261 AB 0.503380659 A C SNP_A-4222423 rs208439 66956275 nonAB 0.136038367 C T SNP_A-4258362 rs992895 66961128 AB 0.401681695 G T SNP_A-4265700 rs2078904 66968787 nonAA 0.421522009 A C SNP_A-1955326 rs2188593 66969330 nonAA 0.468949857 C T SNP_A-4301660 rs10944885 66980703 nonAA 0.446147312 A C SNP_A-1781953 rs6903678 66987929 AA 0.621843717 C T SNP_A-2155680 rs208518 67005222 nonBB 0.320398223 C G SNP_A-1914664 rs9354405 67005296 BB 0.535108771 G T SNP_A-2011807 rs4710584 67010174 BB 0.772685982 A G SNP_A-4225902 rs7776307 67034051 nonAB 0.001204053 C T SNP_A-4302068 rs9453668 67043118 BB 0.710267914 A G SNP_A-2271600 rs7757213 67053332 nonAB 0.019396115 C G SNP_A-1816809 rs7449962 67058797 nonBB 0.155019371 C T SNP_A-1837870 rs1708538 67094767 nonBB 0.233182701 G T SNP_A-2214191 rs1634209 67101187 nonAA 0.763589578 A G SNP_A-1939177 rs1708562 67105278 AB 0.476425329 C G SNP_A-1798466 rs1708561 67105350 nonBB 0.232500588 C T SNP_A-1937587 rs1708558 67106127 BB 0.404541874 C T SNP_A-2258068 rs851861 67111248 BB 0.426728184 C G SNP_A-1846716 rs851860 67111605 BB 0.551286939 A G SNP_A-2297086 rs851859 67111682 nonBB 0.53642737 C T SNP_A-2265033 rs1634186 67126785 AA 0.428705626 C T SNP_A-4222265 rs1101053 67138299 BB 0.184716779 A C SNP_A-2243566 rs9453749 67162197 AA 0.348964445 A G SNP_A-1986279 rs1464074 67180065 nonBB 0.019480989 C T SNP_A-2250414 rs1464072 67180476 nonBB 0.152840767 A G SNP_A-2092453 rs1567793 67180515 nonBB 0.493685519 C T SNP_A-2227103 rs2670402 67204006 nonAA 0.612275732 A G SNP_A-1930404 rs1398808 67205380 nonAA 0.421165298 C T SNP_A-2282605 rs1473877 67209805 nonAA 0.505981179 C T SNP_A-2270551 rs9342552 67211139 BB 0.116774444 A G SNP_A-1835943 rs2812160 67224525 nonBB 0.563122215 A G SNP_A-1807322 rs2670380 67228209 nonAA 0.571011653 A G SNP_A-1892046 rs16898325 67228467 nonAB 0.193386492 A T SNP_A-1986283 rs1355801 67231454 nonBB 0.057590974 C T SNP_A-1847542 rs9294706 67240997 nonAB 0.755365214 A G SNP_A-2311022 rs2812171 67245027 nonAA 0.144870765 G T SNP_A-4245048 rs4631256 67246679 BB 0.351475634 C T SNP_A-1834382 rs6909046 67252166 nonBB 0.829761738 C T SNP_A-1894201 rs2670356 67252310 nonAA 0.876474 C T SNP_A-2158075 rs2812141 67277643 AA 0.640885927 A G SNP_A-1986285 rs2812144 67287396 nonBB 0.06275917 A G SNP_A-4226722 rs1224520 67296344 nonBB 0.227805097 C T SNP_A-2287392 rs16898504 67303202 nonBB 0.371865856 A T SNP_A-1986286 rs1033952 67313735 nonBB 0.075691264 A G SNP_A-2081773 rs7750190 67325355 nonAB 0.720422981 A G SNP_A-1826803 rs9345850 67329439 AA 0.281863109 G T SNP_A-1951754 rs12662737 67331421 BB 0.144509019 A G SNP_A-2258691 rs2148014 67333511 nonBB 0.579904649 C T SNP_A-1841874 rs13194883 67342276 nonAA 0.189553851 C T SNP_A-2103209 rs9354448 67342785 BB 0.415778942 A G SNP_A-2246852 rs9445740 67342888 nonAA 0.12225903 A C SNP_A-2036796 rs4710615 67343887 nonAB 0.586894518 A C SNP_A-4198564 rs9363614 67346658 BB 0.418986508 G T SNP_A-2276296 rs17658544 67346779 nonAB 0.411114231 A G SNP_A-1940914 rs1555821 67362028 nonAB 0.90381755 C T SNP_A-4290242 rs9342564 67382785 nonBB 0.203058287 A T SNP_A-2313640 rs9345858 67386746 AB 0.147368372 A G SNP_A-4252219 rs2504156 67391945 BB 0.650167697 A G SNP_A-1840695 rs183895 67392564 BB 0.603160474 A G SNP_A-1942481 rs1563300 67395762 nonAA 0.280466245 A G SNP_A-4211711 rs1869677 67406990 AB 0.181969602 C T SNP_A-1930419 rs4710324 67408933 AB 0.680804896 C T SNP_A-1986290 rs6910762 67409260 nonAB 0.898493342 A C SNP_A-2217318 rs17527707 67424871 nonBB 0.336080279 A G SNP_A-1880227 rs12527276 67429521 nonAA 0.162053364 A C SNP_A-2096913 rs1037576 67429648 nonAA 0.351391819 A C SNP_A-2054788 rs7764904 67436499 nonAA 0.690320369 A G SNP_A-4265704 rs1869678 67442550 nonAB 0.07364721 C T SNP_A-1840073 rs2352603 67455437 AB 0.130019345 A G SNP_A-2266694 rs12204014 67456669 AA 0.415846403 A C SNP_A-1986292 rs4493734 67459352 nonBB 0.357486066 A G SNP_A-1986293 rs7747972 67460600 AB 0.14131136 A G SNP_A-2198666 rs7761326 67460665 nonBB 0.062918504 C T SNP_A-1986294 rs2100494 67463024 nonBB 0.142356386 A C SNP_A-1828353 rs6909956 67482625 AA 0.198607231 A C SNP_A-1865415 — 67487055 AB 0.174629518 A C SNP_A-4203622 rs6916073 67504953 AB 0.368701315 A G SNP_A-4249410 rs9351595 67525083 AB 0.579684527 C T SNP_A-4227222 rs12202347 67531474 nonBB 0.383486941 A G SNP_A-2025222 rs4710625 67554551 AA 0.225972239 C G SNP_A-2113122 rs10806546 67569403 AB 0.145032883 A T SNP_A-1949934 rs9363639 67569490 nonBB 0.242919791 C G SNP_A-4203608 rs12529103 67576063 AB 0.156407826 C T SNP_A-2221744 rs9360234 67577822 nonBB 0.193145747 C T SNP_A-1927864 rs7743165 67577943 AB 0.151138285 A C SNP_A-4219265 rs9351600 67586556 nonAA 0.052109082 A G SNP_A-2011813 rs4391249 67588711 BB 0.729791965 A G SNP_A-2057150 rs4318854 67601325 AB 0.877693745 C T SNP_A-1841454 rs4580841 67619287 nonAB 0.013868606 A G SNP_A-2233641 rs9354486 67619743 AB 0.741336552 G T SNP_A-1825119 rs4367362 67620159 nonAB 0.023389806 A G SNP_A-2083347 rs4339434 67622969 BB 0.049189623 A G SNP_A-4215142 rs4440442 67623352 AA 0.016680266 C T SNP_A-1986295 rs4132236 67624606 BB 0.021598252 A G SNP_A-1951049 rs9345907 67628274 nonAB 0.142624572 A G SNP_A-1959049 rs9345908 67628441 nonAB 0.154837843 A T SNP_A-1844420 rs9363646 67628674 nonAB 0.362316776 G T SNP_A-2209974 rs9342584 67628733 nonAB 0.203626534 C T SNP_A-2265324 rs9342585 67628959 nonAB 0.094082862 C T SNP_A-1956157 rs9342586 67629022 nonAB 0.133602872 A G SNP_A-1807163 rs7749074 67631479 nonAB 0.108801678 C T SNP_A-4259504 rs7773507 67632117 nonAB 0.117244617 A G SNP_A-4272583 rs9351604 67632329 nonAB 0.127328082 C G SNP_A-2159325 rs9351605 67632535 nonAB 0.131556367 A G SNP_A-4197295 rs9354492 67632813 BB 0.357095183 A T SNP_A-4222876 rs6913994 67635043 AA 0.671269565 A G SNP_A-1937055 rs9453912 67653009 BB 0.671038158 A G SNP_A-4222982 rs9294720 67668486 BB 0.663769033 G T SNP_A-2228267 rs7772529 67668648 AA 0.677458462 G T SNP_A-2096160 rs9345929 67691396 nonAA 0.614308483 G T SNP_A-2068542 rs4257844 67692405 BB 0.592867859 A G SNP_A-2197892 rs4147069 67709608 nonAA 0.283916906 A T SNP_A-2211798 rs12529449 67709838 AB 0.407025755 C T SNP_A-1956530 rs6930795 67717579 nonAA 0.173522369 A G SNP_A-2176155 rs9345935 67721287 nonBB 0.262215437 A G SNP_A-2039561 rs4373347 67729617 nonBB 0.248207962 A C SNP_A-2190184 rs9345943 67738293 BB 0.170382664 C T SNP_A-1912155 rs10944941 67738476 nonBB 0.009480535 A G SNP_A-1942665 rs9354515 67740780 AA 0.247647109 C G SNP_A-1792361 rs9453944 67744804 AB 0.331283095 A G SNP_A-2074794 rs9453945 67744825 AB 0.600361333 A G SNP_A-4196394 rs4416661 67745004 AB 0.053885363 C T SNP_A-4273241 rs1947417 67763231 nonBB 0.118972558 C T SNP_A-2046648 rs9453963 67770561 AB 0.291378768 A G SNP_A-2164620 rs10944944 67782897 nonAA 0.003899835 A G SNP_A-2156618 rs6930520 67788376 nonBB 0.715462562 G T SNP_A-1922191 rs12210443 67803641 AB 0.120030719 C T SNP_A-4256067 rs7746422 67810012 nonAA 0.176786085 C T SNP_A-4271007 rs2502273 67810028 AA 0.198326315 G T SNP_A-2169127 rs7765154 67810156 BB 0.173179279 A C SNP_A-2062463 rs2503951 67821780 nonAA 0.311489566 C T SNP_A-1829752 rs9454007 67843097 nonAA 0.111934359 A C SNP_A-2091834 rs1947413 67844420 AB 0.848674959 C G SNP_A-2152285 rs2444666 67844610 AA 0.181406319 C T SNP_A-1873497 rs1377705 67847494 nonAA 0.093967153 C G SNP_A-1893710 rs2262774 67852545 BB 0.22630909 C T SNP_A-4193347 rs2503903 67859644 nonBB 0.687204623 A G SNP_A-1986298 rs9294736 67861137 nonAA 0.285949609 A G SNP_A-1802217 rs2262773 67875733 nonBB 0.706899921 A T SNP_A-2240807 rs2167984 67875837 AB 0.716322253 C T SNP_A-1986299 rs1377715 67889189 nonAA 0.456009969 C T SNP_A-2255506 rs12665811 67899814 nonAA 0.386518083 C T SNP_A-2230857 rs17539557 67933211 nonAA 0.40943496 A G SNP_A-2207654 rs9351638 67938018 BB 0.025364211 A T SNP_A-4239686 rs4582362 67953240 BB 0.619223604 C T SNP_A-2182665 rs9294744 67953940 BB 0.28694409 A G SNP_A-4228547 rs1380039 67957360 BB 0.45154921 A G SNP_A-1795282 rs6455225 67986868 AB 0.221108447 C T SNP_A-1835113 rs9342632 68012296 nonAA 0.449342024 C T SNP_A-2042042 rs6927570 68013116 AB 0.332054635 A G SNP_A-2214902 rs9363732 68016553 BB 0.35325772 A G SNP_A-4265709 rs1903058 68022441 nonBB 0.263624228 A G SNP_A-2059426 rs1380042 68022798 AB 0.199142797 C T SNP_A-1871981 rs9360283 68045248 nonBB 0.107016414 A T SNP_A-1883648 rs12529871 68051892 nonAB 0.024891699 A C SNP_A-2260201 rs9363741 68085762 nonBB 0.714245056 A G SNP_A-4220095 rs10944983 68095015 AA 0.121995543 C T SNP_A-4253625 rs4518480 68111102 BB 0.607619589 A G SNP_A-1873784 rs7765600 68128859 nonBB 0.70413356 C T SNP_A-2088208 rs4472333 68154792 nonAA 0.085981401 A C SNP_A-2039342 rs2166656 68154890 nonAA 0.095872573 A G SNP_A-1842671 rs9454128 68162044 nonBB 0.032954255 A G SNP_A-1918809 rs1447136 68168816 nonAA 0.03860696 G T SNP_A-4222185 rs1447137 68168899 nonBB 0.031238496 A G SNP_A-2190666 rs1447138 68168916 nonAA 0.034098227 A C SNP_A-1881805 rs9351662 68197504 BB 0.261576779 G T SNP_A-4265712 rs9294768 68218149 AA 0.27162598 G T SNP_A-2115322 rs9342648 68272068 AA 0.090563204 A G SNP_A-2011816 rs1418903 68326677 BB 0.069113798 C T SNP_A-2080305 rs856818 68334871 AB 0.070590599 A G SNP_A-4276121 rs2747146 68355495 BB 0.127145051 C G SNP_A-4278225 rs2747148 68358862 nonAB 0.348010932 C T SNP_A-1986311 rs2747156 68371284 BB 0.29857778 G T SNP_A-1986312 rs2818113 68398350 nonAB 0.119132517 A G SNP_A-1887553 rs11961947 68412365 nonAB 0.072847527 A G SNP_A-1814455 rs2179964 68414245 nonAB 0.242585771 G T SNP_A-1951401 rs2816902 68428695 nonBB 0.583499331 A C SNP_A-2310345 rs2818103 68432617 AB 0.400077745 A G SNP_A-1847145 rs12200729 68440919 nonAA 0.154538678 A G SNP_A-2105178 rs12207706 68440963 AA 0.523701043 C T SNP_A-2248482 rs2493374 68454951 BB 0.371449439 A G SNP_A-4246325 rs13209120 68457255 nonAB 0.126481364 C T SNP_A-1845690 rs9454233 68459204 AB 0.488846596 C T SNP_A-4231448 rs2818114 68464683 BB 0.023873075 A G SNP_A-1889479 rs9445899 68474413 AB 0.384874076 C T SNP_A-2140829 rs6930022 68502644 BB 0.502307287 A T SNP_A-1845037 rs4132510 68522631 BB 0.249644517 C T SNP_A-1853383 rs4541731 68532252 nonBB 0.344570751 C T SNP_A-1894669 rs9363804 68542471 AA 0.300361672 C T SNP_A-1986313 rs9294774 68543635 BB 0.003851141 C T SNP_A-1986314 rs4131870 68549169 AA 0.345007124 C T SNP_A-4228954 rs6455249 68561399 AA 0.004040529 A G SNP_A-2133277 rs6910355 68561881 AA 0.004387613 A G SNP_A-2197265 rs9454286 68562671 BB 0.003985839 C G SNP_A-2025392 rs12203654 68563436 nonAA 0.260529856 A C SNP_A-1956525 rs6906512 68563980 AA 0.004040529 A T SNP_A-2011817 rs6913371 68565666 nonAA 0.313545736 A G SNP_A-4286405 rs1913477 68583232 AA 0.206848621 A G SNP_A-4295818 rs1913478 68583437 nonBB 0.21074883 C T SNP_A-2278290 rs7760466 68589686 AB 0.144626707 A G SNP_A-2240239 rs16880598 68602023 AA 0.188543071 C T SNP_A-4279153 rs2203381 68605628 AA 0.281792769 A G SNP_A-4295103 rs9354637 68643530 BB 0.224070713 C T SNP_A-1781814 rs9454346 68651892 BB 0.362672809 C T SNP_A-1805813 rs10945033 68655380 nonBB 0.094614433 A G SNP_A-2153824 rs10945038 68664465 nonAB 0.229542991 A G SNP_A-1925991 rs10945039 68666005 nonAB 0.495374235 C T SNP_A-2236917 rs9454374 68677397 AA 0.725441032 C G SNP_A-2147648 rs9454388 68694538 nonAB 0.417806066 A G SNP_A-2028380 rs9445946 68699466 nonAA 0.334000299 A C SNP_A-4211718 rs9294781 68703877 nonBB 0.052693383 A G SNP_A-4259283 rs7748806 68710365 BB 0.14686197 C T SNP_A-2153874 rs7771084 68742455 nonBB 0.084014969 A G SNP_A-2126945 rs1877779 68744069 BB 0.231245678 C T SNP_A-4258034 rs1079471 68746094 nonAA 0.083618664 C T SNP_A-1823155 rs11758293 68748355 nonAA 0.579494531 A C SNP_A-1931161 rs6918336 68755007 AA 0.218452668 C T SNP_A-4246230 rs6904134 68757817 BB 0.081461098 A G SNP_A-1953490 rs6455261 68764810 AB 0.393681146 A T SNP_A-1817126 rs4706313 68785785 nonAA 0.233887469 G T SNP_A-1858769 rs4706314 68785851 nonAA 0.753436788 C T SNP_A-2175249 rs2124267 68785979 AB 0.126799908 A G SNP_A-4278993 rs4707476 68787717 nonBB 0.561916634 A T SNP_A-1986316 rs4707479 68787830 AB 0.468545179 A G SNP_A-1882975 rs1378456 68804070 BB 0.492255619 A G SNP_A-2011818 rs4311477 68806041 nonAA 0.538728908 G T SNP_A-4236765 rs10945052 68809335 BB 0.435200881 C T SNP_A-1909368 rs9454421 68820455 AB 0.328717189 G T SNP_A-1835393 rs9354665 68833034 AA 0.613923615 C T SNP_A-2061528 rs4707839 68856959 AA 0.76365803 A G SNP_A-4203963 rs7753361 68857216 BB 0.452270737 A G SNP_A-1883107 rs2061117 68861088 BB 0.828491277 A G SNP_A-1821902 rs7746319 68867684 AA 0.526542438 C G SNP_A-1986318 rs777608 68877195 nonBB 0.319926751 C T SNP_A-1843440 rs1454715 68883959 BB 0.564892274 G T SNP_A-1807108 rs13216403 68885000 AA 0.328352954 A C SNP_A-4237089 rs4707858 68887583 BB 0.699839656 G T SNP_A-2248800 rs777632 68889857 AB 0.065625928 A G SNP_A-1952435 rs9454430 68893559 AA 0.027532325 C T SNP_A-1810514 rs1083338 68911998 nonBB 4.12612E−07 A G SNP_A-1878533 rs10455650 68914971 nonAA 0.219680984 A G SNP_A-1833857 rs4357093 68924471 AB 0.023297867 C T SNP_A-1890727 rs777649 68925053 nonAA 0.008993603 A C SNP_A-1892939 rs9360320 68931796 AB 0.000160941 A C SNP_A-2284478 rs9346128 68945739 AB 0.493734985 A T SNP_A-1826944 rs701662 68946749 nonAA 0.475418776 A G SNP_A-1820941 rs7454318 68972611 nonBB 0.514851315 A G SNP_A-1986320 rs9294789 68977021 nonAA 0.763553882 G T SNP_A-4224312 rs9360322 68987349 BB 0.56100183 C T SNP_A-1817175 rs9445980 68987459 nonAA 0.067032568 A G SNP_A-1986321 rs778017 68989905 AB 0.059469935 A G SNP_A-1824424 rs2924823 68990861 AA 0.31153523 A T SNP_A-2058335 rs1993329 68992781 nonBB 0.117076194 C T SNP_A-1952045 rs1993330 68993112 nonBB 0.14070107 C T SNP_A-1888898 rs1454721 69000303 AA 0.052102189 A G SNP_A-2032140 rs2603687 69001129 AA 0.143328527 C T SNP_A-2303872 rs2786578 69006095 BB 0.049325261 A G SNP_A-4217539 rs4707962 69015945 BB 0.20569452 A G SNP_A-2057079 rs6919859 69024600 BB 0.08649071 C T SNP_A-1813596 rs1454729 69025003 AA 0.335283907 A G SNP_A-2296644 rs9454451 69028199 BB 0.081307616 A G SNP_A-2168603 rs2184928 69044566 BB 0.18566116 A G SNP_A-2154765 rs10945072 69049649 AA 0.484176227 C T SNP_A-4197020 rs7750882 69064295 AA 0.071063307 A C SNP_A-2280180 rs9346146 69084649 AA 0.343506966 A G SNP_A-1849260 rs1388051 69086145 BB 0.193000865 A G SNP_A-2143797 rs2341484 69089538 nonBB 0.054734965 A C SNP_A-1833677 rs1158811 69090289 nonBB 0.106813302 A G SNP_A-2158451 rs7756182 69095347 BB 0.052580631 A G SNP_A-1986325 rs9363896 69096028 BB 0.273997765 A T SNP_A-2022548 rs1490619 69114853 BB 0.441977481 A C SNP_A-2024346 rs3902666 69115229 BB 0.446447339 A G SNP_A-1838735 rs4708047 69131964 AB 0.024262517 A G SNP_A-4259570 rs2029516 69134708 AB 0.096338846 C T SNP_A-2269890 rs1907149 69138866 AA 0.807356148 A G SNP_A-1874667 rs9346173 69140243 nonBB 0.153766142 A G SNP_A-1924580 rs9342706 69165194 nonAB 0.211174481 G T SNP_A-1920594 rs1388053 69172360 nonAA 0.371779781 C T SNP_A-1832341 rs10945110 69181323 nonAB 0.168791567 A G SNP_A-2270836 rs9354735 69187420 nonAB 0.206539339 C T SNP_A-2120489 rs9454511 69187803 AA 0.329593016 A G SNP_A-2035277 rs2341762 69193923 nonAA 0.388089444 A G SNP_A-1931552 rs3011917 69202748 AA 0.186828573 A C SNP_A-2061740 rs3011918 69206541 nonAB 0.574286976 A G SNP_A-2158365 rs1388056 69233497 AB 0.154997616 A C SNP_A-1816026 rs12208783 69233602 nonAB 0.271023414 G T SNP_A-4194440 rs9354760 69238978 AA 0.256571578 C T SNP_A-1821079 rs9454527 69246326 nonAB 0.391488629 C T SNP_A-1871649 rs13195148 69253950 nonAA 0.173624205 C T SNP_A-2253627 rs9342711 69253971 AA 0.505715623 A G SNP_A-2086009 rs1508668 69265165 BB 0.611789217 C T SNP_A-1921256 rs6455280 69266503 AA 0.864734509 C T SNP_A-1854616 rs10806600 69267214 BB 0.248613262 A C SNP_A-4269716 rs4587131 69279955 nonAB 0.08470264 A C SNP_A-1986328 rs7356811 69311024 nonBB 0.734229873 C T SNP_A-4211721 rs10498866 69311173 nonAB 0.08470264 C T SNP_A-4265715 rs6904357 69311500 nonAB 0.137358975 C T SNP_A-2156873 rs10455670 69347352 AB 0.124406821 C T SNP_A-2213885 rs7748176 69348086 nonAA 0.301162435 C T SNP_A-1808349 rs7761592 69348223 BB 0.145357001 A G SNP_A-1827869 rs9351730 69351206 nonBB 0.336531891 C T SNP_A-1884209 rs9354792 69363616 AA 0.222347599 C T SNP_A-2275127 rs9454590 69377171 nonBB 0.413900869 C T SNP_A-4235770 rs9454591 69377245 BB 0.507309037 A G SNP_A-4231725 rs4708197 69377258 nonAB 0.08891776 A G SNP_A-4256530 rs9454592 69377455 nonAB 0.332886628 C T SNP_A-2088631 rs2802710 69378216 nonAB 0.219810926 G T SNP_A-1831646 rs10945134 69412170 BB 0.459264769 A G SNP_A-4211722 rs2802684 69454318 AA 0.498620793 A G SNP_A-1833170 rs2064389 69482532 AA 0.181230192 C T SNP_A-4211723 rs715294 69483117 AA 0.15915365 C T SNP_A-4240085 rs2802676 69483590 nonAA 0.443315749 A T SNP_A-1986332 rs9342730 69492227 BB 0.465269095 A G SNP_A-1986333 rs2206836 69518162 BB 0.547315159 A G SNP_A-1986334 rs10484791 69521107 AB 0.927224238 A G SNP_A-1944938 rs9454616 69543012 BB 0.198468902 A G SNP_A-2146272 rs9346240 69544601 nonAB 0.366758217 A C SNP_A-2075137 rs9446057 69545130 BB 0.12870168 C G SNP_A-2062606 rs6920537 69560087 AA 0.218972835 A G SNP_A-1815365 rs9360361 69565919 BB 0.129043538 A G SNP_A-1814446 rs10806605 69569069 nonBB 0.347459283 A T SNP_A-1938288 rs492444 69584586 BB 0.142447534 A G SNP_A-2074047 rs11963528 69584891 AB 0.725748475 A C SNP_A-2116985 rs571299 69597671 AB 0.322957999 A G SNP_A-1908491 rs577328 69598052 AB 0.328204465 A G SNP_A-2099983 rs497240 69599012 AB 0.174054447 A G SNP_A-2074652 rs551876 69602150 AB 0.311359709 C T SNP_A-2178081 rs482005 69602514 AB 0.129944515 A C SNP_A-1807155 rs555588 69602576 AB 0.157965551 A G SNP_A-2045722 rs2224011 69611902 AB 0.154184325 A C SNP_A-2030772 rs491928 69616860 nonAA 0.048336367 A G SNP_A-2169189 rs492823 69616956 nonAA 0.054845091 A G SNP_A-2099669 rs493682 69617025 nonBB 0.031388918 C T SNP_A-2038034 rs536054 69617501 nonAA 0.048336367 A C SNP_A-1986335 rs507326 69621367 nonAA 0.084181083 G T SNP_A-2126762 rs526501 69631765 nonAA 0.064260669 A C SNP_A-1834995 rs542600 69632331 nonBB 0.029930938 C T SNP_A-1956352 rs544398 69632524 nonBB 0.03833799 C T SNP_A-1787918 rs556592 69632721 AA 0.938540927 C T SNP_A-1837824 rs523962 69635461 nonAA 0.163669121 A C SNP_A-4230709 rs13217051 69646968 nonBB 0.245832954 C T SNP_A-1986336 rs7760666 69678581 nonAA 0.173437314 C G SNP_A-2180913 rs17476598 69690023 AA 0.036182149 C T SNP_A-1986337 rs2184723 69703807 AA 0.308062915 A G SNP_A-4237559 rs13215030 69705481 AA 0.29491441 C G SNP_A-2207627 rs13201188 69705545 AA 0.52439831 C T SNP_A-2140790 rs7767423 69709768 nonBB 0.111939351 G T SNP_A-1986338 rs1932615 69713729 AA 0.318024631 A G SNP_A-4223698 rs3798974 69732559 nonAB 0.444776938 A G SNP_A-4242644 rs1006997 69734043 BB 0.784750645 C T SNP_A-2295673 rs3823064 69738338 nonAA 0.207301881 A G SNP_A-2035872 rs3798979 69738381 nonAA 0.227214308 A G SNP_A-2051035 rs1415031 69757118 AB 0.272724923 C G SNP_A-2231832 rs3798995 69757481 nonBB 0.293574761 A C SNP_A-2260112 rs13205016 69763910 AB 0.340070069 A G SNP_A-1956833 rs1415030 69767438 nonBB 0.755244613 A G SNP_A-2027159 rs9446083 69768622 AB 0.533010934 A G SNP_A-2114787 rs9454674 69777487 AA 0.149455524 C G SNP_A-2098481 rs9446085 69783083 BB 0.356857325 C T SNP_A-1986340 rs10485430 69785173 AA 0.304100586 C T SNP_A-1986341 rs1415035 69787173 nonAB 0.706142627 C T SNP_A-2091923 rs1889878 69793014 BB 0.356857325 C T SNP_A-2197746 rs7743332 69803749 AA 0.401936715 C T SNP_A-4256562 rs688606 69840895 nonBB 0.288753084 A T SNP_A-1959874 rs4706854 69857763 BB 0.046260609 A G SNP_A-1986343 rs10485427 69873172 nonAB 0.001127204 A G SNP_A-1986344 rs964664 69873584 nonBB 0.0194823 A G SNP_A-1836498 rs7759645 69874050 AA 0.524865891 C T SNP_A-2263575 rs1842743 69882402 nonBB 0.015309939 C G SNP_A-2164122 rs1482326 69901489 nonAA 0.588728993 A G SNP_A-2238216 rs314218 69912418 AA 0.151751036 A G SNP_A-2052026 rs7739401 69915651 nonAA 0.013215186 A T SNP_A-2196893 rs9294824 69928005 nonBB 0.123040805 A G SNP_A-4265717 rs6926403 69929922 AB 0.771879811 C T SNP_A-1876463 rs16900556 69937268 AB 0.664551707 G T SNP_A-4251849 rs7741707 69937498 AB 0.208083342 C T SNP_A-2136973 rs779473 69981003 AA 0.582045567 A G SNP_A-4301796 rs1877427 69984990 AB 0.536453316 C T SNP_A-1986346 rs779467 69988140 nonBB 0.065518522 C T SNP_A-4211724 — 69988477 AB 0.666411578 C T SNP_A-1986348 rs1849304 69994898 AA 0.115734734 C G SNP_A-1787417 rs16900583 69997676 AB 0.359291789 C T SNP_A-4200751 rs779464 69997808 BB 0.574193997 A G ¹Official SNP nomenclature according to NCBI db SNP version 126, May 2006. ²Chromosomal position based on the NCBI Build 36.1, March 2006. ³P value of genotype having highest QT values versus all other genotypes.

SNPs useful in the practice of the invention are selected from among SNPs listed in Table 1 and can be used singly or in any combination of two or more.

A genotype of GG at the rs1083338 locus was found to most accurately predict a predisposition to QT prolongation. This genotype is included amongst all genotypes associated with a predisposition to QT prolongation. Therefore, individuals having a genotype of GG at the rs1083338 locus may be considered predisposed to QT prolongation following the administration of a compound capable of prolonging the QT interval.

Since the QT interval changes with changes in heart rate, the QT interval is often measured as a corrected QT (QTc) interval. Any number of formulas may be employed to calculate the QTc, including, for example, the Fridericia formula (QTcF), the Bazett formula (QTcB), and the Rautaharju formula (QTp), among others. In the studies described herein, QT was calculated using the Fridericia formula. However, the present invention includes the use of any such formula or method for calculating a QTc or an uncorrected QT.

As noted above, a large number of compounds are known or suspected to be capable of inducing QT prolongation in some individuals, including individuals not suffering from LQTS. Such compounds may include compounds of Formula (1):

wherein:

R is, independently, hydrogen, lower alkyl, lower alkoxy, hydroxyl, carboxyl, lower hydroxyketone, lower alkanol, hydroxyl acetic acid, pyruvic acid, ethanediol, chlorine, fluorine, bromine, iodine, amino, lower mono or dialkylamino, nitro, lower alkyl thio, trifluoromethoxy, cyano, acylamino, trifluoromethyl, trifluoroacetyl, aminocarbonyl, monoaklylaminocarbonyl, dialkylaminocarbonyl, formyl,

alkyl is lower alkyl, branched or straight and saturated or unsaturated;

acyl is lower alkyl or lower alkyloxy bonded through a carbonyl;

aryl is phenyl or phenyl substituted with at least one group, R₅, wherein each R₅ is, independently, hydrogen, lower alkyl, lower alkoxy, hydroxy, chlorine, fluorine, bromine, iodine, lower monoalkylamino, lower dialkylamino, nitro, cyano, trifluoromethyl, or trifluoromethoxy;

heteroaryl is a five- or six-membered aryl ring having at least one heteroatom, Q₃, wherein each Q₃ is, independently, —O—, —S—, —N(H)—, or —C(H)═N—

W is CH₂ or CHR₈ or N—R₉;

R₁ is —H, lower alkyl, —OH, halo, lower alkoxy, trifluormethyl, nitro, or amino;

R₂ is C₂-C₅ alkylene, alkenylene (cis or trans), or alkynylene, optionally substituted by at least one C₁-C₆ linear alkyl group, phenyl group or

where Z₁ is lower alkyl, —OH, lower alkoxy, —CF₃, —NO₂, —NH₂, or halogen; R₃ is lower alkyl or hydrogen; R₇ is hydrogen, lower alkyl, or acyl; R₈ is lower alkyl; R₉ is hydroxy, lower alkoxy, or —NHR₁₀; R₁₀ is hydrogen, lower alkyl, C₁-C₃ acyl, aryl,

X₁, X₂, and X₃ are, independently, —O—, —S—, ═N—, or —N(R₃)—, or X₁ and X₂ are not covalently bound to each other and are, independently, —OH, ═O, —R₃, or ═NR₃; lower is 1-4 carbon atoms; m is 1, 2, or 3; and n is 1 or 2.

The compound may further include a compound of Formula (1), wherein:

R is —C(O)CH₂OH, —CH(OH)C(O)CH₂OH, —C(O)OH, CH(OH)CH₃, or C(O)CH₃; R₁ is halo;

X₁ and X₂ are different and are ═O, —OH, ═N—, or —O—;

R₂ is C₂-C₄ alkylene or alkenylene;

R₃ is hydrogen, methyl, or ethyl;

X₃ is —O—; and

R is Formula (1A):

In a further embodiment, the compound may be iloperidone, which is also referred to as 1-[4-[3-[4-(6-fluoro-1,2-benzisoxazol-3-yl)-1-piperidinyl]propoxy]-3-methoxyphenyl]ethanone, as shown in Formula 1B:

Iloperidone is disclosed in U.S. Pat. Nos. 5,364,866, 5,658,911, and 6,140,345, each of which is incorporated herein by reference. Metabolites of iloperidone may also be capable of prolonging a QT interval. Metabolites of Iloperidone, e.g., 1-[4-[3-[4-(6-Fluoro-1,2-benzisoxazol-3-yl)-1-piperidinyl]propoxy]-3-methoxyphenyl]ethanol, as shown in Formula 1C:

are described in International Patent Application Publication No. WO03020707, which is also incorporated herein by reference.

Other iloperidone metabolites include: 1-[4-[3-[4-(6-Fluoro-1,2-benzisoxazol-3-yl)-1-piperidinyl]propoxy]-3-hydroxyphenyl]ethanone; 1-[4-[3-[4-(6-Fluoro-1,2-benzisoxazol-3-yl)-1-piperidinyl]propoxy]-3-methoxyphenyl]-2-hydroxyethanone; 4-[3-[4-(6-Fluoro-1,2-benzisoxazol-3-yl)-1-piperidinyl]propoxy]-3-hydroxy-α-methylbenzene methanol; 4-[3-[4-(6-Fluoro-1,2-benzisoxazol-3-yl)-1-piperidinyl]propoxyl-2-hydroxy-5-methoxy-α-methylbenzenemethanol; 1-[4-[3-[4-(6-Fluoro-1,2-benzisoxazol-3-yl)-1-piperidinyl]propoxy]-2-hydroxy-5-methoxyphenyl]ethanone; and 1-[4-[3-[4-(6-Fluoro-1,2-benzisoxazol-3-yl)-1-piperidinyl]propoxy]-2,5-dihydroxyphenyl]ethanone. See U.S. Pat. No. 5,364,866 and International Patent Application Publication Nos. WO9309276 and WO9511680, which are incorporated herein by reference.

Using the genotypes at the SNP loci above, it is possible, with a high degree of certainty, to predict an individual's predisposition to QT prolongation. Table 2 below shows the results of a study of 174 individuals, each of whom was genotyped at the rs1083338 locus and their QT interval measured following the oral administration of 24 mg/day B.I.D. of iloperidone for a period of two weeks.

TABLE 2 QT Prolongation and Presence or Absence of a Genotype for SNP_A-1810514, rs1083338 Associated with a Predisposition to QT Prolongation negative positive Change Threshold Low QT High QT Odds p predictive predictive (msec) −test +test −test +test Ratio value sensitivity specificity value value QT > 5 59 7 78 39 4.21 0.0012 0.33 0.89 0.43 0.85 QT > 15 93 17 44 29 3.61 0.0003 0.40 0.85 0.68 0.63 QT > 30 123 32 14 14 3.84 0.0016 0.50 0.79 0.90 0.30

As can be seen in Table 2, an individual's BAI3 sequence at the SNP_A-1810514, rs1083338 locus is highly predictive of whether the individual will experience QT prolongation following the administration of iloperidone. For example, using the lowest threshold of a change in QTc interval (between baseline and the end of the second week) greater than 5 milliseconds (normal QTc intervals are between 0.30 and 0.44 seconds for males and between 0.30 and 0.45 for females), 39 of those individuals with the GG genotype (test is considered positive if the genotype for SNP_A-1810514, rs1083338 is GG) experienced QT prolongation while only seven such individuals did not. The resulting sensitivity (probability that the individual will have a SNP genotype associated with a predisposition to QT prolongation, given that he/she experienced QT prolongation) of 0.33, specificity (probability that the individual will not have a SNP genotype associated with a predisposition to QT prolongation, given that he/she did not experience QT prolongation) of 0.89, negative predictive value (probability that the individual will not experience QT prolongation, given that he/she does not have a SNP genotype associated with a predisposition to QT prolongation) of 0.43, and a positive predictive value (probability that the individual will experience QT prolongation, given that he/she has a SNP genotype associated with a predisposition to QT prolongation) of 0.85, permit one to predict with great accuracy that an individual possessing the GG genotype is likely to experience QT prolongation.

The use of higher thresholds (i.e., QTs greater than 15 and 30 milliseconds) yielded markedly increased negative predictive values (0.68 and 0.90, respectively). The associated decrease in positive predictive values, from 0.85 for QTs greater than 5 milliseconds to 0.30 for QTs greater than 30 milliseconds) suggests that additional factors affect more severe QT prolongation.

As the data in Table 2 show, an individual's BAI3 sequence at the SNP loci above may be used to predict whether an individual is predisposed to QT prolongation due to the administration of a compound capable of prolonging the QT interval. That is, individuals having a genotype of GG at the rs1083338 locus may reliably be predicted to experience a prolonged QT interval (i.e., a change in QT interval of at least 5 milliseconds) following the administration of a compound capable of prolonging the QT interval. Similarly, individuals having a genotype other than GG at the rs1083338 locus may reliably be predicted to not experience severe QT prolongation (i.e., a change in QT interval of greater than 15 milliseconds) following the administration of a compound capable of prolonging the QT interval.

The ability to make such predictions may be used in deciding whether to treat an individual with a particular compound and/or in determining the dosage appropriate for the individual. For example, an individual predicted to experience QT prolongation may be treated with an alternative compound not known or suspected to cause QT prolongation or may be administered a lower dose of a compound capable of causing QT prolongation than would be administered to an individual not predicted to experience QT prolongation.

The present invention also includes the administration of another compound useful in treating LQTS, in addition to one or more of the compounds above. Compounds useful in treating LQTS and/or preventing cardiac events resulting from LQTS, include, for example, beta blockers, such as propranolol, nadolol, atenolol, metoprolol.

The present invention also includes the prediction of an individual's predisposition for QT prolongation based on one or more of the SNP loci above in combination with the individual's genotype or gene sequence at one or more additional genes or loci. For example, International Patent Application Publication No. WO2006039663, incorporated herein by reference, describes a method of treating an individual with a compound capable of inducing QT prolongation based on the individual's CYP2D6 genotype. Other genotypes and/or gene sequences may similarly be used in combination with the SNP loci above, including those associated with LQTS. It should also be understood that the present invention includes the characterization of an expression product of the BAI3 gene rather than, or in addition to, the determination of one or more SNP genotypes within the BAI3 gene. For example, by determining a sequence of an mRNA strand transcribed from the BAI3 gene, it is possible to determine the sequence of the BAI3 gene itself and, as described above, determine whether the BAI3 gene sequence is associated with a predisposition to QT prolongation.

Similarly, by properly characterizing a functional peptide or protein, including the BAI3 enzyme, translated from the mRNA strand above, it is possible to determine the sequence of the BAI3 gene itself and, as described above, determine whether the BAI3 gene sequence is associated with a predisposition to QT prolongation. In addition, the present invention includes determining whether a compound is capable of prolonging a QT interval in an individual. This may be done, for example, by measuring a change in QT interval in a test organism (e.g., human, animal model, cell line) known to possess a BAI3 genotype associated with a predisposition to QT prolongation following the administration of a quantity of compound under study.

Preferably, the compound is also administered to a test organism known to possess a BAI3 genotype not associated with a predisposition to QT prolongation.

Thus, in addition to other illustrative embodiments, this invention can be seen to comprise one or more of the following illustrative embodiments:

1. A method of administering to an individual a compound capable of prolonging the individual's QT interval, the method comprising:

determining at least a portion of an individual's BAI3 gene sequence; and

in the case that a portion of the individual's BAI3 gene sequence is associated with an increased risk of QT prolongation, administering to the individual a quantity of the compound less than would be administered to an individual having a BAI3 gene sequence not associated with an increased risk of QT prolongation.

2. The method of embodiment 1, wherein determining includes determining the individual's genotype at the rs1083338 locus.

3. The method of embodiment 2, wherein the genotype associated with an increased risk of QT prolongation is GG.

4. The method of embodiment 1, further comprising: determining the individual's CYP2D6 genotype.

5. The method of embodiment 1, wherein the compound is selected from a group consisting of: amiodarone, arsenic trioxide, bepridil, chloroquine, chlorpromazine, cisapride, clarithromycin, disopyramide, dofetilide, domperidone, droperidol, erythromycin, halofantrine, haloperidol, ibutilide, iloperidone, levomethadyl, mesoridazine, methadone, pentamidine, pimozide, procainamide, quinidine, sotalol, sparfloxacin, thioridazine; alfuzosin, amantadine, azithromycin, chloral hydrate, clozapine, dolasetron, felbamate, flecainide, foscarnet, fosphenytoin, gatifloxacin, gemifloxacin, granisetron, indapamide, isradipine, levofloxacin, lithium, moexipril, moxifloxacin, nicardipine, octreotide, ofloxacin, ondansetron, quetiapine, ranolazine, risperidone, roxithromycin, tacrolimus, tamoxifen, telithromycin, tizanidine, vardenafil, venlafaxine, voriconazole, ziprasidone; albuterol, amitriptyline, amoxapine, amphetamine, dextroamphetamine, atomoxetine, chloroquine, ciprofloxacin, citalopram, clomipramine, cocaine, desipramine, dexmethylphenidate, dobutamine, dopamine, doxepin, ephedrine, epinephrine, fenfluramine, fluconazole, fluoxetine, galantamine, imipramine, isoproterenol, itraconazole, ketoconazole, levalbuterol, metaproterenol, methylphenidate, mexiletine, midodrine, norepinephrine, nortriptyline, paroxetine, phentermine, phenylephrine, phenylpropanolamine, protriptyline, pseudoephedrine, ritodrine, salmeterol, sertraline, sibutramine, solifenacin, terbutaline, tolterodine, trimethoprim-sulfa, trimipramine, and metabolites, pharmaceutically-acceptable salts, and combinations thereof. 6. The method of embodiment 5, wherein the compound has the formula:

wherein:

R is, independently, hydrogen, lower alkyl, lower alkoxy, hydroxyl, carboxyl, lower hydroxyketone, lower alkanol, hydroxyl acetic acid, pyruvic acid, ethanediol, chlorine, fluorine, bromine, iodine, amino, lower mono or dialkylamino, nitro, lower alkyl thio, trifluoromethoxy, cyano, acylamino, trifluoromethyl, trifluoroacetyl, aminocarbonyl, monoaklylaminocarbonyl, dialkylaminocarbonyl, formyl,

alkyl is lower alkyl, branched or straight and saturated or unsaturated;

acyl is lower alkyl or lower alkyloxy bonded through a carbonyl;

aryl is phenyl or phenyl substituted with at least one group, R₅, wherein each R₅ is, independently, hydrogen, lower alkyl, lower alkoxy, hydroxy, chlorine, fluorine, bromine, iodine, lower monoalkylamino, lower dialkylamino, nitro, cyano, trifluoromethyl, or trifluoromethoxy;

heteroaryl is a five- or six-membered aryl ring having at least one heteroatom, Q₃, wherein each Q₃ is, independently, —O—, —S—, —N(H)—, or —C(H)═N—

W is CH₂ or CHR₈ or N—R₉;

R₁ is —H, lower alkyl, —OH, halo, lower alkoxy, trifluormethyl, nitro, or amino;

R₂ is C₂-C₅ alkylene, alkenylene (cis or trans), or alkynylene, optionally substituted by at least one C₁-C₆ linear alkyl group, phenyl group or

where Z₁ is lower alkyl, —OH, lower alkoxy, —CF₃, —NO₂, —NH₂, or halogen;

R₃ is lower alkyl or hydrogen;

R₇ is hydrogen, lower alkyl, or acyl;

R₈ is lower alkyl;

R₉ is hydroxy, lower alkoxy, or —NHR₁₀;

R₁₀ is hydrogen, lower alkyl, C₁-C₃ acyl, aryl,

X₁, X₂, and X₃ are, independently, —O—, —S—, ═N—, or —N(R₃)—, or X₁ and X₂ are not covalently bound to each other and are, independently, —OH, ═O, —R₃, or ═NR₃; lower is 1-4 carbon atoms;

m is 1, 2, or 3; and

n is 1 or 2.

7. The method of embodiment 6, wherein:

R is —C(O)CH₂OH, —CH(OH)C(O)CH₂OH, —C(O)OH, CH(OH)CH₃, or C(O)CH₃;

R₁ is halo;

X₁ and X₂ are different and are ═O, —OH, ═N—, or —O—;

R₂ is C₂-C₄ alkylene or alkenylene;

R₃ is hydrogen, methyl, or ethyl;

X₃ is —O—;

R is

8. The method of embodiment 7, wherein the compound of Formula 1 is 1-[4-[3-[4-(6-fluoro-1,2-benzisoxazol-3-yl)-1-piperidinyl]propoxy]-3-methoxyphenyl]ethanone, as shown in Formula 1B:

9. The method of embodiment 7, wherein the compound of Formula 1 is 1-[4-[3-[4-(6-Fluoro-1,2-benzisoxazol-3-yl)-1-piperidinyl]propoxy]-3-methoxyphenyl]ethanol, as shown in Formula 1C:

10. A method of determining whether an individual is predisposed to prolongation of the QT interval, the method comprising:

determining at least a portion of an individual's BAI3 gene sequence.

11. The method of embodiment 10, further comprising:

in the case that a portion of the individual's BAI3 gene sequence is associated with an increased risk of QT prolongation, administering to the individual a compound not known or suspected to cause QT prolongation.

12. The method of embodiment 10, wherein determining includes determining the individual's genotype at the rs1083338 locus.

13. The method of embodiment 12, wherein the genotype associated with an increased risk of QT prolongation is GG.

14. The method of embodiment 10, further comprising: determining the individual's CYP2D6 genotype.

15. A method of administering a compound capable of prolonging a QT interval to an individual suffering from long QT syndrome (LQTS), the method comprising:

determining at least a portion of an individual's BAI3 gene sequence; and

administering to the individual a quantity of the compound based on the individual's BAI3 gene sequence.

16. The method of embodiment 15, wherein determining includes determining the individual's genotype at the rs1083338 locus.

17. The method of embodiment 16, wherein the genotype associated with an increased risk of QT prolongation is GG.

18. The method of embodiment 15, further comprising:

determining the individual's CYP2D6 genotype.

19. The method of embodiment 15, wherein the compound is selected from a group consisting of: amiodarone, arsenic trioxide, bepridil, chloroquine, chlorpromazine, cisapride, clarithromycin, disopyramide, dofetilide, domperidone, droperidol, erythromycin, halofantrine, haloperidol, ibutilide, iloperidone, levomethadyl, mesoridazine, methadone, pentamidine, pimozide, procainamide, quinidine, sotalol, sparfloxacin, thioridazine; alfuzosin, amantadine, azithromycin, chloral hydrate, clozapine, dolasetron, felbamate, flecainide, foscarnet, fosphenytoin, gatifloxacin, gemifloxacin, granisetron, indapamide, isradipine, levofloxacin, lithium, moexipril, moxifloxacin, nicardipine, octreotide, ofloxacin, ondansetron, quetiapine, ranolazine, risperidone, roxithromycin, tacrolimus, tamoxifen, telithromycin, tizanidine, vardenafil, venlafaxine, voriconazole, ziprasidone; albuterol, amitriptyline, amoxapine, amphetamine, dextroamphetamine, atomoxetine, chloroquine, ciprofloxacin, citalopram, clomipramine, cocaine, desipramine, dexmethylphenidate, dobutamine, dopamine, doxepin, ephedrine, epinephrine, fenfluramine, fluconazole, fluoxetine, galantamine, imipramine, isoproterenol, itraconazole, ketoconazole, levalbuterol, metaproterenol, methylphenidate, mexiletine, midodrine, norepinephrine, nortriptyline, paroxetine, phentermine, phenylephrine, phenylpropanolamine, protriptyline, pseudoephedrine, ritodrine, salmeterol, sertraline, sibutramine, solifenacin, terbutaline, tolterodine, trimethoprim-sulfa, trimipramine, and metabolites, pharmaceutically-acceptable salts, and combinations thereof. 20. The method of embodiment 19, wherein the compound has the formula:

wherein:

R is, independently, hydrogen, lower alkyl, lower alkoxy, hydroxyl, carboxyl, lower hydroxyketone, lower alkanol, hydroxyl acetic acid, pyruvic acid, ethanediol, chlorine, fluorine, bromine, iodine, amino, lower mono or dialkylamino, nitro, lower alkyl thio, trifluoromethoxy, cyano, acylamino, trifluoromethyl, trifluoroacetyl, aminocarbonyl, monoaklylaminocarbonyl, dialkylaminocarbonyl, formyl,

alkyl is lower alkyl, branched or straight and saturated or unsaturated;

acyl is lower alkyl or lower alkyloxy bonded through a carbonyl;

aryl is phenyl or phenyl substituted with at least one group, R₅, wherein each R₅ is, independently, hydrogen, lower alkyl, lower alkoxy, hydroxy, chlorine, fluorine, bromine, iodine, lower monoalkylamino, lower dialkylamino, nitro, cyano, trifluoromethyl, or trifluoromethoxy;

heteroaryl is a five- or six-membered aryl ring having at least one heteroatom, Q₃, wherein each Q₃ is, independently, —O—, —S—, —N(H)—, or —C(H)═N—

W is CH₂ or CHR₈ or N—R₉;

R₁ is —H, lower alkyl, —OH, halo, lower alkoxy, trifluormethyl, nitro, or amino;

R₂ is C₂-C₅ alkylene, alkenylene (cis or trans), or alkynylene, optionally substituted by at least one C₁-C₆ linear alkyl group, phenyl group or

where Z₁ is lower alkyl, —OH, lower alkoxy, —CF₃, —NO₂, —NH₂, or halogen;

R₃ is lower alkyl or hydrogen;

R₇ is hydrogen, lower alkyl, or acyl;

R₈ is lower alkyl;

R₉ is hydroxy, lower alkoxy, or —NHR₁₀;

R₁₀ is hydrogen, lower alkyl, C₁-C₃ acyl, aryl,

X₁, X₂, and X₃ are, independently, —O—, —S—, ═N—, or —N(R₃)—, or X₁ and X₂ are not covalently bound to each other and are, independently, —OH, ═O, —R₃, or ═NR₃; lower is 1-4 carbon atoms;

m is 1, 2, or 3; and

n is 1 or 2.

21. The method of embodiment 20, wherein:

R is —C(O)CH₂OH, —CH(OH)C(O)CH₂OH, —C(O)OH, CH(OH)CH₃, or C(O)CH₃;

R₁ is halo;

X₁ and X₂ are different and are ═O, —OH, ═N—, or —O—;

R₂ is C₂-C₄ alkylene or alkenylene;

R₃ is hydrogen, methyl, or ethyl;

X₃ is —O—;

R is

22. The method of embodiment 21, wherein the compound of Formula 1 is 1-[4-[3-[4-(6-fluoro-1,2-benzisoxazol-3-yl)-1-piperidinyl]propoxy]-3-methoxyphenyl]ethanone, as shown in Formula 1B:

23. The method of embodiment 21, wherein the compound of Formula 1 is 1-[4-[3-[4-(6-Fluoro-1,2-benzisoxazol-3-yl)-1-piperidinyl]propoxy]-3-methoxyphenyl]ethanol, as shown in Formula 1C:

24. A method of administering to an individual a compound capable of prolonging the individual's QT interval, the method comprising:

characterizing an expression product of an individual's BAI3 gene; and

in the case that the characterized expression product is associated with an increased risk of QT prolongation, administering to the individual a quantity of the compound less than would be administered to an individual having an expression product not associated with an increased risk of QT prolongation.

25. The method of embodiment 24, wherein the expression product includes at least one expression product selected from a group consisting of: mRNA, a peptide, and a protein.

26. A method of determining whether an individual is predisposed to prolongation of the QT interval, the method comprising:

characterizing an expression product of an individual's BAI3 gene.

27. The method of embodiment 26, wherein the expression product includes at least one expression product selected from a group consisting of: mRNA, a peptide, and a protein.

28. A method of administering a compound capable of prolonging a QT interval to an individual suffering from long QT syndrome (LQTS), the method comprising:

characterizing an expression product of an individual's BAI3 gene; and

administering to the individual a quantity of the compound based on the characterized expression product.

29. The method of embodiment 28, wherein the expression product includes at least one expression product selected from a group consisting of: mRNA, a peptide, and a protein.

30. A method of determining whether a compound is capable of prolonging a QT interval in an individual, the method comprising:

measuring an expression product of the individual's BAI3 gene;

administering to the individual a quantity of the compound;

remeasuring the expression product of the individual's BAI3 gene; and

determining whether the compound is capable of prolonging the individual's QT interval based on a difference in the measurements of the expression product of the individual's BAI3 gene.

31. The method of embodiment 30, wherein the expression product includes at least one expression product selected from a group consisting of: mRNA, a peptide, and a protein.

32. A method of determining whether a compound is capable of prolonging a QT interval in an individual, the method comprising:

measuring a QT interval of each of a plurality of test organisms, the plurality including a first test organism having a BAI3 genotype associated with a predisposition for prolongation of QT interval and a second organism having a BAI3 genotype not associated with a predisposition for prolongation of QT interval;

administering a quantity of the compound to each of the plurality of test organisms;

remeasuring a QT interval of at least the first test organism; and

determining that the compound is capable of prolonging a QT interval in an individual in the case that the remeasured QT interval is greater than the measured QT interval.

33. The method of embodiment 32, wherein each of the plurality of test organisms is selected from a group consisting of: humans, animals, and cell lines.

The foregoing description of various aspects of the invention has been presented for purposes of illustration and description. It is not intended to be exhaustive or to limit the invention to the precise form disclosed, and obviously, many modifications and variations are possible. Such modifications and variations that may be apparent to a person skilled in the art are intended to be included within the scope of the invention as defined by the accompanying claims. 

What is claimed is:
 1. A method of administering a compound to a human individual, wherein the compound is iloperidone, a metabolite of iloperidone, or a pharmaceutically acceptable salt of iloperidone or metabolite thereof, the method comprising: determining the individual's BAI3 genotype at a single nucleotide polymorphism (SNP) locus selected from the group consisting of rs7776307, rs10944944, rs9294774, rs9360320, and rs10485427; and administering a first quantity of the compound if the individual's BAI3 genotype is associated with increased risk of QT prolongation and is CT at rs7776307, AA at rs10944944, non-TT at rs9294774, non-AC at rs9360320, or AG at rs10485427, or administering a second quantity of the compound if the individual's BAI3 genotype is non-CT at rs7776307, non-AA at rs10944944, TT at rs9294774, AC at rs9360320, or non-AG at rs10485427; wherein the first quantity of the compound is less than the second quantity of the compound.
 2. The method of claim 1, further comprising determining the individual's CYP2D6 genotype.
 3. The method of claim 1, wherein the compound is iloperidone or a pharmaceutically acceptable salt thereof.
 4. A method of administering a compound to a human individual suffering from long QT syndrome (LQTS), wherein the compound is iloperidone, a metabolite of iloperidone, or a pharmaceutically acceptable salt of iloperidone or metabolite thereof, the method comprising: determining the individual's BAI3 genotype at a single nucleotide polymorphism (SNP) locus selected from the group consisting of rs7776307, rs10944944, rs9294774, rs9360320, and rs10485427; and administering a first quantity of the compound if the individual's BAI3 genotype is associated with increased risk of QT prolongation and is CT at rs7776307, AA at rs10944944, non-TT at rs9294774, non-AC at rs9360320, or AG at rs10485427, or administering a second quantity of the compound if the individual's BAI3 genotype is non-CT at rs7776307, non-AA at rs10944944, TT at rs9294774, AC at rs9360320, or non-AG at rs10485427; wherein the first quantity of the compound is less than the second quantity of the compound.
 5. The method of claim 4, further comprising determining the individual's CYP2D6 genotype.
 6. The method of claim 4, wherein the compound is iloperidone or a pharmaceutically acceptable salt thereof.
 7. The method of claim 1, wherein the compound is a metabolite of iloperidone or a pharmaceutically acceptable salt thereof, wherein the metabolite is 1-[4-[3-[4-(6-Fluoro-1,2-benzisoxazol-3-yl)-1-piperidinyl]propoxy]-3-methoxyphenyl]ethanol.
 8. The method of claim 4, wherein the compound is a metabolite of iloperidone or a pharmaceutically acceptable salt thereof, wherein the metabolite is 1-[4-[3-[4-(6-Fluoro-1,2-benzisoxazol-3-yl)-1-piperidinyl]propoxy]-3-methoxyphenyl]ethanol.
 9. The method of claim 1, wherein the second quantity of the compound is 24 mg/day.
 10. The method of claim 4, wherein the second quantity of the compound is 24 mg/day. 